ArticleFrontiers in genetics2021
Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
- Data-intensive immune network modelling for One Health.Briefings in bioinformatics · 2026Review
- Integrated Bulk and Single-Cell Transcriptomic Analysis Followed by Clinical Validation Reveal Programmed Cell Death-Related Shared Molecular Signatures in OA and MDD.International journal of molecular sciences · 2026Article
- AMF-induced salinity tolerance in durum wheat is associated with transcriptomic modulation of the Cation/Calcium Exchanger 1 (CCX1).Mycorrhiza · 2026Article
- The Intersection of m6A Methylation and Immune Response in PCOS: A Bioinformatics Perspective.Immunity, inflammation and disease · 2026Article
- Leveraging bioinformatics approaches for drug repositioning in space radiation protection.PloS one · 2026Article
- Muscle Organoids Reveal Exercise-Like Contractions Rapidly Promote Muscle Health Via Lamtor1's Signaling to Both AMPK and mTOR.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Shared Genetic Architecture Among Severe Mental Disorders: A System Biology Approach Based on Protein-Protein Interaction.Brain and behavior · 2025Article
- A Systems Biology Approach for Prioritizing ASD Genes in Large or Noisy Datasets.International journal of molecular sciences · 2025Article
- Decoding the Tumor Microenvironment of Myoepithelial Cells in Triple-Negative Breast Cancer Through Single-Cell and Transcriptomic Sequencing and Establishing a Prognostic Model Based on Key Myoepithelial Cell Genes.International journal of genomics · 2025Article
- Identification of key genes associated with muscle atrophy after spinal cord injury and experimental verification in rats.Frontiers in immunology · 2025Article
- Gene signatures associated with exosomes as diagnostic markers of postpartum depression and their role in immune infiltration.Frontiers in endocrinology · 2025Article
- Spectral divergence prioritizes key classes, genes, and pathways shared between substance use disorders and cardiovascular disease.Frontiers in neuroscience · 2025Article
- Deciphering the Role of Necroptosis-Related Long Non-coding RNAs in Hepatocellular Carcinoma: A Necroptosis-Related lncRNA-Based Signature to Predict the Prognosis of Hepatocellular Carcinoma.Applied biochemistry and biotechnology · 2025Article
- Spatial transcriptomics reveals gene interactions and signaling pathway dynamics in rat embryos with anorectal malformation.Cell biology and toxicology · 2024Article
- Preconditioning exercise reduces brain damage of ischemic stroke in rats via PI3K-AKT pathway by bioinformatic analysis.Experimental brain research · 2024Article
- Article
- Single-cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines inMicrobiology spectrum · 2024Article
- GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases.NPJ systems biology and applications · 2024Article
- Evaluation of Near-Infrared Laser Effects on 143B Cells: A System Biology Approach.Journal of lasers in medical sciences · 2024Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene set enrichment analysis (GSEA) is a powerful tool to associate a disease phenotype to a group of genes/proteins. GSEA attributes a specific weight to each gene/protein in the input list that depends on a metric of choice, which is usually represented by quantitative expression data. However, expression data are not always available. Here, GSEA based on betweenness centrality of a protein-protein interaction (PPI) network is described and applied to two cases, where an expression metric is missing. First, personalized PPI networks were generated from genes displaying alterations (assessed by array comparative genomic hybridization and whole exome sequencing) in four probands bearing a 16p13.11 microdeletion in common and several other point variants. Patients showed disease phenotypes linked to neurodevelopment. All networks were assembled around a cluster of first interactors of altered genes with high betweenness centrality. All four clusters included genes known to be involved in neurodevelopmental disorders with different centrality. Moreover, the GSEA results pointed out to the evidence of "cell cycle" among enriched pathways. Second, a large interaction network obtained by merging proteomics studies on three neurodegenerative disorders was analyzed from the topological point of view. We observed that most central proteins are often linked to Parkinson's disease. The selection of these proteins improved the specificity of GSEA, with "Metabolism of amino acids and derivatives" and "Cellular response to stress or external stimuli" as top-ranked enriched pathways. In conclusion, betweenness centrality revealed to be a suitable metric for GSEA. Thus, centrality-based GSEA represents an opportunity for precision medicine and network medicine.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.